Init

1"""
2Utility modules for nf-core pipeline deployment.
3
4Modules:
5    ncbi_utils: NCBI/GEO/SRA data fetching and download utilities
6    file_discovery: Find FASTQ, BAM, and CRAM files
7    sample_inference: Extract sample info, detect tumor/normal
8    validators: Validate samplesheets before writing
9"""
10
11# NCBI utilities for GEO/SRA data acquisition
12from .ncbi_utils import (
13    check_network_access,
14    fetch_geo_metadata,
15    fetch_sra_study_accession,
16    fetch_sra_run_info,
17    fetch_sra_run_info_detailed,
18    fetch_bioproject_from_geo,
19    fetch_ena_fastq_urls,
20    download_file,
21    fetch_pubmed_metadata,
22    format_file_size,
23    estimate_download_size,
24    group_samples_by_type,
25    format_sample_groups_table,
26)
27
28# File discovery utilities
29from .file_discovery import discover_files, FileInfo, count_files_by_type
30
31# Sample inference utilities
32from .sample_inference import (
33    extract_sample_info,
34    infer_tumor_normal_status,
35    match_read_pairs,
36    extract_replicate_number
37)
38
39# Validation utilities
40from .validators import validate_samplesheet, ValidationResult
41
42__all__ = [
43    # ncbi_utils
44    'check_network_access',
45    'fetch_geo_metadata',
46    'fetch_sra_study_accession',
47    'fetch_sra_run_info',
48    'fetch_sra_run_info_detailed',
49    'fetch_bioproject_from_geo',
50    'fetch_ena_fastq_urls',
51    'download_file',
52    'fetch_pubmed_metadata',
53    'format_file_size',
54    'estimate_download_size',
55    'group_samples_by_type',
56    'format_sample_groups_table',
57    # file_discovery
58    'discover_files',
59    'FileInfo',
60    'count_files_by_type',
61    # sample_inference
62    'extract_sample_info',
63    'infer_tumor_normal_status',
64    'match_read_pairs',
65    'extract_replicate_number',
66    # validators
67    'validate_samplesheet',
68    'ValidationResult',
69]